MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b2066 b1241 b4384 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1033 b0261 b2799 b3945 b1602 b2913 b3915 b2492 b0904 b1380 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.500166 (mmol/gDw/h)
  Minimum Production Rate : 0.293743 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.396241
  EX_o2_e : 286.491777
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.401751
  EX_pi_e : 0.776206
  EX_so4_e : 0.125952
  EX_k_e : 0.097629
  EX_mg2_e : 0.004339
  EX_ca2_e : 0.002603
  EX_cl_e : 0.002603
  EX_cu2_e : 0.000355
  EX_mn2_e : 0.000346
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991967
  EX_h2o_e : 550.912008
  EX_co2_e : 37.708021
  Auxiliary production reaction : 0.293743
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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